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At least 19 recordsLinked to original sources
PubMed1977

Endonucleolytic cleavage of parental DNA and T4 late-gene expression: distribution analysis of single-strand and double-strand breaks.

In order to investigate the dependency of late transcription on concurrent DNA replication during bacteriophage T4 development, we analyzed the endonucleolytic cleavage kinetics of the DNA of a T4 mutant lacking DNA polymerase, DNA ligase and exonuclease by using the sucrose gradient sedimentation technique. Our results can be summarized as follows. 1. The single-strand endonucleolytic cleavage of the T4 mutant DNA is not a random process. 2. The number of single-strand nicks reaches a plateau level of 10--12 nicks/molecule. 3. The occurrence of a double-strand break is delayed and their number is at any time lower than the number of single-strand nicks. 4. The circular permutation T4 genome, as computer-simulated by the Monte Carlo method, produces a smoothing of the discrete distribution which would be expected if nicks were localized in the promoter sites of late transcription units. We conclude that our findings support the model which relates single-strand DNA nicks to the late transcription initiation sites.

Centrifugation, Density Gradient↗
PubMed1979

Evidence for endonucleolytic cleavage at the 5'-proximal segment of the trp messenger RNA in Escherichia coli.

The 5'-proximal trp leader RNA segment (about 5S) decays at 2 to 3 times slower rates than the distal trp mRNA sequence. This has been demonstrated by employing the deletion mutants which lack a large portion of the structural genes but retain the promoter-proximal region of the trp operon. Relative stability of the leader RNA is not merely due to the presence of an untranslatable region in the segment; the internal untranslatable segment of trp mRNA downstream from the nonsense alteration site of a double mutant trpAD28.trpE9758 decays as fast as the normal trp mRNA sequence. These results suggest that the trp mRNA is endonucleolytically cleaved to yield the small 5'-proximal leader RNA segment before the distal mRNA decays and that the leader RNA sequence is not subject to usual mode of mRNA decay in the 5' to 3' direction.

DNA, Viral↗
PubMed1977

A site-specific single-strand endonuclease from the eukaryote Chlamydomonas.

We have found a unique deoxyribonuclease in extracts of the eukaryotic green alga Chlamydomonas. When incubated with viral DNA from adenovirus-2, this enzyme produces discrete fragments that form bands upon electrophoresis in an agarose gel. Site specificity of the enzymatic cleavage examined by identifying the 5'-terminal nucleotides in cleaved adenovirus-2 DNA and by studies with synthetic polynucleotides of defined sequence, indicates that the initial endonucleolytic cleavage occurs at a site containing a deoxythymidine residue. Electron microscopy of cleaved adenovirus-2 DNA revealed single-strand segments within duplex DNA. We propose that the enzyme acts by making initial site-specific single-strand incisions, followed by subsequent excision on the same strand, producing a gapped duplex molecule; and that double-strand scissions result from limited occurrence of overlapping single-strand gaps on complementary strands.

Base Sequence↗
PubMed1978

Complementary sequences 1700 nucleotides apart form a ribonuclease III cleavage site in Escherichia coli ribosomal precursor RNA.

The nucleotide sequence of Escherichia coli DNA at both ends of the gene for 16S rRNA has been determined for two rRNA operons, rrnD and rrnX. The 400 nucleotides we have examined exhibit only one base change between rrnD and rrnX. Within the 160 nucleotides that precede mature 16S rRNA sequences are cleavage sites for several E. coli endonucleases, including RNase III. A 240-nucleotide segment encompassing the 16S 3' end contains another RNase III site and the point of presumed RNase P scission at the 5' end of tRNA1Ile, the first tRNA appearing in the 16-23S spacer region of rrnD and rrnX. Most importantly, the DNA sequences predict that regions flanking the 16S gene in the rRNA primary transcript extensively base pair to form a double-helical structure whose hairpin loop includes the entire mature 16S molecule; within this structure is a 26-base-pair stem containing the two sequences at which RNase III action generates the 5' and 3' ends of a previously characterized precursor to 16S rRNA. Although our proposed secondary structure for this RNase III site is superficially dissimilar to previously described cleavage sites in the T7 early mRNA precursor, certain common features may constitute signals for RNase III recognition. The suggestion that distant portions of an RNA molecule can form a secondary structure within which specific endonucleolytic cleavages occur may have mechanistic implications for the joining of noncontiguous portions of gene sequences evident in several eukaryotic mRNAs.

Base Sequence↗
PubMed2025

RNase III cleavage sites spread across splice junctions enforce sequential snoRNA processing.

Small nucleolar RNAs (snoRNAs) are a class of eukaryotic non-coding RNA molecules whose precursor transcripts are capped and polyadenylated. However, these end modifications are detrimental to snoRNA function and must be removed, a process typically involving excision from introns and/or endonucleolytic cleavage. For RNA precursors that host multiple snoRNAs, the sequence of maturation events is potentially important, but not well understood. Here, we report a new mode of maturation concerning snoRNA pairs that are co-hosted in the intron and the adjacent 3' exon of a precursor transcript. For a snoRNA pair with this arrangement in Schizosaccharomyces pombe, we found that the sequence surrounding an exon-exon junction within their precursor transcript folds into a hairpin after splicing of the intron. This hairpin recruits the RNase III ortholog Pac1, which participates in the maturation of the downstream snoRNA by cleaving the precursor. Our findings suggest that conditional RNase III cleavage signals hidden in an exon-exon junction evolved to enforce sequential snoRNA processing. Sequence analysis suggests that this mechanism is conserved in animals and plants.

RNA, Small Nucleolar↗
PubMed1979

Adenovirus early function required for protection of viral and cellular DNA.

Studies were done to characterize a DNA-negative temperature-sensitive (ts) mutant of human adenovirus type 2, H2 ts111. The temperature-sensitive defect, which was reversible on shift-down in the absence of protein synthesis, was expressed as early as 2 h postinfection, and the results of density-labeling experiments are in agreement with at least a DNA replication initiation block. On shift-up, after allowing viral DNA synthesis at permissive temperatures, the newly synthesized viral DNA and the mature viral DNA were cleaved into fragments which sedimented as a broad peak with a mean coefficient of 10-12S. This cleavage was more marked in the presence of hydroxyurea as the DNA synthesis inhibitor. Parental DNA in infected cells was degraded to a much lesser extent regardless of the incubation temperature. In contrast, the parental DNA was strongly degraded when early gene expression was permitted at 33 degrees C before shift-up to 39.5 degrees C. Furthermore, cellular DNA was also degraded at 39.5 degrees C in ts111-infected cells, the rate of cleavage being related to the multiplicity of infection. This cleavage effect, which did not seem to be related to penton base-associated endonuclease activity, was also enhanced when early gene expression was allowed at 33 degrees C before shift-up. The ts111 defect, which was related to an initiation block and endonucleolytic cleavage of viral and cellular DNA, seemed to correspond to a single mutation. The implication of the ts111 gene product in protection of viral and cellular DNA by way of a DNase-inhibitory function is discussed.

Adenoviruses, Human↗
PubMed1979

Total synthesis of a tyrosine suppressor transfer RNA gene. XVII. Transcription, in vitro, of the synthetic gene and processing of the primary transcript to transfer RNA.

Primer- and promoter-dependent transcription of the synthesis gene had been studied. Primer-dependent transcription gave, as a major product, an end-to-end transcript which was strand-specific. The transcript was characterized rigorously by two-dimensional separation and analysis of the oligonucleotides formed on digestion with T1-RNase and pancreatic RNase and by nearest neighbor analyses of the oligonucleotides obtained when different alpha-32P-labeled ribonucleoside triphosphates were used as substrates. Minor products accompanying the major transcript were characterized similarly. The major transcript, when treated with an Escherichia coli S-100 extract, was processed to the tRNATyr with correct 5'- and 3'-ends. The nucleolytic cleavages occurring at the 3'-end were characterized. In promoter-dependent transcription, transcription of a restriction fragment containing phi80psu+III gene and the synthetic gene with and without the promoter were compared. Transcription of the synthetic gene was promoter-dependent and strand-specific, the initiation of transcription occurring at the same point as previously found in vivo. Although the synthetic gene contains only 16 base pairs corresponding to the natural sequence following the C-C-A end, processing of the transcript at the 3'-end occurred normally, the endonucleolytic cleavage being followed by exonucleolytic cleavages. The products of promoter-dependent transcription were completely characterized. An examination of the base modifications of the primary transcript during treatment of the latter with E. coli S-100 extract showed couplete modification of uridine to pseudouridine and partial methylation of uridine to ribosylthymine in TpsiCG sequence and partial formation of pseudouridine in the anticodon loop. However, hardly any formation of 2'-O-methylguanosine or of 2-methylthio-6-isopentenyl adenosine could be detected.

Base Sequence↗
PubMed1978

Carcinogen-induced DNA repair in nucleotide-permeable Escherichia coli cells. Analysis of DNA repair induced by carcinogenic K-region epoxides and 1,2,3,4-diepoxybutane.

Ether-permeabilized (nucleotide-permeable) Escherichia coli cells exhibited DNA excision repair when exposed to the following carcinogenic K-region epoxides: 7-methyl- and 7,12-dimethyl-benz[a]anthracene-5,6-oxide, chrysene-5,6-oxide and benzo[a]pyrene-4,5-oxide. This DNA excision repair was missing in uvr A and uvr B mutant cells. The K-region epoxide phenanthrene-9,10-oxide was ineffective in all E. coli strains tested. In contrast to the K-region epoxides which where found active only in wild type cells, 1,2,3,4-diepoxybutane and the 6,7-epoxides of the tumor promoter TPA (12-O-tetradecanoyl-phorbol-13-acetate) elicited DNA repair in uvrA, uvrB mutant cells as well. Enzymic activities catalyzing particular repair steps were identified by determining a) repair polymerization and b) size reduction of denatured DNA. A) An easily quantifiable effect in E. coli wild type cells was epoxide-induced repair polymerization. None of the K-region epoxides tested stimulated DNA repair synthesis in uvrA, uvrB mutant cells, indicating that the uvrA-, uvrB-controlled UV-endonuclease initiated excision repair by cleaving epoxide-damaged DNA. 1,2,3,4-Diepoxybutane and the TPA-6,7-oxides induced DNA repair polymerization in uvr-deficient cells, although to a lesser extent than in wild type cells, suggesting the involvement of uvr-independent incision steps. None of the epoxides induced repair polymerization in a mutant (polA107) lacking the 5'--3'exonucleolytic activity of DNA polymerase I (exonuclease VI). The absence of any repair polymerization in the polA107 mutant indicates that the exonuclease VI plays a central role in removing epoxide-damaged nucleotides. As evidenced by greatly reduced levels of repair polymerization measured in polA1 cells, DNA polymerase I was the main polymerizing enzyme. b) As a consequence of treatment with 7-methyl-benz[a]anthracene-5,6-oxide, DNA from wild type cells, contrary to uvrA mutant cells, showed size reduction after denaturation and sedimentation in alkaline sucrose gradients. This is explained by repair-specific endonucleolytic cleavage of damaged DNA. The incision required the presence of ATP indicating that functional UV-endonuclease needs ATP as a cofactor.

Carcinogens↗
PubMed1979

The primary transcription product of a silkworm alanine tRNA gene: identification of in vitro sites of initiation, termination and processing.

A 13.5 Kb fragment of Bombyx mori DNA containing a single tRNA2Ala gene has been cloned, and transcribed in vitro with Xenopus germinal vesicle extracts. The primary transcription product of the tRNA2Ala gene has been isolated and shown to possess an unprocessed triphosphorylated 5' terminus. Products resulting from processing of this transcript have also been isolated and characterized. Complete nucleotide sequence analysis of this cloned alanine tRNA gene and its primary transcript shows that transcription initiates three nucleotides away from the mature tRNA2Ala 5' end and terminates in a U cluster 22 nucleotides beyond the last encoded 3' nucleotide of the mature species. Sequence determination of the products of in vitro maturation shows that in contrast to the tRNA processing mechanism characteristic of procaryotes, the extra 3'-nucleotides in this silkworm tRNA precursor are removed by a single endonucleolytic cleavage.

Alanine↗
PubMed1978

Purification and characterization of a DNA single strand specific endonculease from human cells.

An endonuclease with DNA single-strand specificity has been purified from KB cells. The enzyme has a pH optimum at 9.2, requires Mg2+ for activity, and is inhibited by mono- or divalent cations. Its sedimentation coefficient of 4.6 S is based on sucrose gradient sedimentation, and it has a molecular weight of 54 000 as determined by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate. The enzyme specifically catalyzes the endonucleolytic cleavage of denatured DNA, yielding acid-soluble oligonucleotides which contain 5'-phosphoryl termini. The rate of hydrolysis of poly(dT) is approximately eightfold greater than that observed with denatured DNA, although the Km for both substrates is 1.74 X 10(-5) M. The relative rates of hydrolysis of homopolymers by the endonuclease are: poly(dG) greater than poly(dT) greater than poly(dA) greater than poly (dC). Purified enzyme preparations also hydrolyze poly(U), releasing acid-soluble products. This activity cosediments in sucrose gradients with the DNA endonuclease activity, suggesting that both activities are contained in the same enzyme molecule.

Cations, Divalent↗
PubMed1978

Structure and processing of yeast precursor tRNAs containing intervening sequences.

We have isolated a precursor of yeast tRNATyr and shown that it contains an intervening sequence identical to that found in the gene for tRNATyr. The conformation of pre-tRNATyr is similar to that of mature tRNATyr except for the anticodon loop. The loop is sensitive to endonucleolytic cleavage by S1 nuclease near to the ends of the intervening sequence. This pre-tRNA is functionally inactive as it cannot be aminoacylated and the anticodon is not accessible for hydrogen bonding. A crude nuclear extract from yeast contains an excision-ligase activity which will process pre-tRNATyr into mature tRNATyr.

Anticodon↗
PubMed1978

Purification and properties of a manganese-stimulated deoxyribonuclease produced during sporulation of Bacillus subtilis.

A DNAase (deoxyribonuclease) was isolated from culture supernatants of sporulating Bacillus subtilis 168. The purified enzyme migrated as a single band during polyacrylamide-gel electrophoresis. The enzyme differs from other DNAases of B. subtilis in molecular weight, metal-ion requirement and mode of action. The enzyme was inactive in the absence of metal ions, and exhibited optimum activity with 10 mM-Mn2+, although Mg2+, Cd2+ and Co2+ could also permit some activity. The pH optimum for the enzyme was pH 7.5, and it degraded linear-duplex DNA or closed-circular-duplex DNA to acid-soluble material. There was little or no activity on single-stranded DNA or rRNA. Sucrose-gradient analysis of the products of DNAase action on bacteriophage T7 DNA showed that endonucleolytic cleavage had occurred by the introduction of single-strand breaks in both strands of the duplex. The molecular weight of the enzyme was determined, by gel filtration on Sephadex G-75, to be 12000.

Bacillus subtilis↗
PubMed1975

Carcinogen-induced DNA repair in nucleotide-permeable Escherichia coli cells. Induction of DNA repair by the carcinogens methyl and ethyl nitrosourea and methyl methanesulfonate.

Ether-permeabilized (nucleotide-permeable) cells of Escherichia coli show excision repair of their DNA after having been exposed to the carcinogens N-methyl-N-nitrosourea (MeNOUr), N-ethyl-N-nitrosourea (EtNOUr) and methyl methanesulfonate (MeSO2OMe) which are known to bind covalently to DNA. Defect mutations in genes uvrA, uvrB, uvrC, recA, recB, recC and rep did not inhibit this excision repair. Enzymic activities involved in this repair were identified by measuring size reduction of DNA, DNA degradation to acid-soluble nucleotides and repair polymerization. 1. In permeabilized cells methyl and ethyl nitrosourea induced endonucleolytic cleavage of endogenous DNA, as determined by size reduction of denatured DNA in neutral and alkaline sucrose gradients. An enzymic activity from E. coli K-12 cell extracts was purified (greater than 2000-fold) and was found to cleave preferentially methyl-nitrosourea-treated DNA and to convert the methylated supercoiled DNA duplex (RFI) of phage phiX 174 into the nicked circular form. 2. Degradation of alkylated cellular DNA to acid solubility was diminished in a mutant lacking the 5' leads to 3' exonucleolytic activity of DNA polymerase I but was not affected in a mutant which lacked the DNA polymerizing but retained the 5' leads 3' exonucleolytic activity of DNA polymerase I. 3. An easily measurable effect is carcinogen-induced repair polymerization, making it suitable for detection of covalent binding of carcinogens and potentially carcinogenic compounds.

Carcinogens↗
PubMed1977

An endonuclease activity of venom phosphodiesterase specific for single-stranded and superhelical DNA.

A homogeneous preparation of venom phosphodiesterase from Crotalus adamanteus possesses an intrinsic endonuclease activity, specific for superhelical (form I) and single-stranded DNA. The phosphodiesterase degrades single-stranded T7 DNA by endonucleolytic cleavages. Duplex T7 DNA is hydrolyzed by the liberation of acid-soluble products simultaneously from the 3' and 5' termini but without demonstrable internal scissions in duplex regions. Since venom phosphodiesterase is known to hydrolyze oligonucleotides stepwise from the 3' termini, the cleavage at the 5' end of duplex T7 DNA is ascribed to an endonuclease activity. Form I PM2 DNA is nicked to yield first relaxed circles and then linear DNA which is subsequently hydrolyzed only from the chain termini. The linear duplex DNA intermediates consist of a discrete series of fragments (11 are usually resolved on agarose gels) with initial molecular weights ranging from 6.3 x 10(6) (the intact PM2 DNA size) to approximately 1 x 10(6). The cleavage of the form I molecule must, therefore, occur at a limited number of unique sites. The enzyme also cleaves nonsuperhelical, covalently closed circular PM2 DNA but at a 10(4) times slower rate. Both the endonuclease activity on form I DNA and the known exonuclease activity co-migrate on polyacrtkanude gels, are optimally active at pH 9, are stimulated by small concentrations of Mg2+, and are similarly inactivated by heat, reducing agents, and EDTA.

DNA, Single-Stranded↗
PubMed2025

Global Profiling and Analysis of 5' Monophosphorylated mRNA Decay Intermediates.

During RNA turnover, the action of endo- and exo-ribonucleases can yield RNA decay intermediates with specific 5' ends. These RNA decay intermediates have been demonstrated to be the outcome of decapping, microRNA-directed endo-cleavage, or the protected fragments of ribosomes and exon-junction complexes. Therefore, global analysis of RNA decay intermediates can facilitate studies of many RNA decay pathways. In this chapter, we describe a high-throughput sequencing protocol named parallel analysis of RNA ends (PARE), which allows genome-wide profiling of 5' monophosphorylated mRNA decay intermediates from plants or other eukaryotes. Also, we present the tools and scripts necessary for the proper analysis of RNA degradome data obtained from the PARE method. Details and modifications of library construction procedures and bioinformatic analyses to optimize sequencing quality and cope with emerging sequencing platforms and findings are highlighted.

RNA Stability↗
PubMed1977

Partial purification and properties of a ribosomal RNA maturation endonuclease from Bacillus subtilis.

Data are presented on the partial purification and properties of a 5 S ribosomal RNA maturation nuclease, termed RNase M5, from Bacillus subtillis 168. RNase M5 specifically cleaves 21 and 42 nucleotides, respectively, from the 5' and 3' termini of a 5 S rRNA precursor to yield the mature (116 nucleotides) 5 S rRNA. The cleavage is endonucleolytic with the formation of 5'-phosphoryl and 3'-hydroxyl groups. Enzyme action requires divalent cations, which may be furnished by either certain metals or by polyamines. The activity is separable into two components both of which are required for activity. It appears that the same nuclease excises the 5'- and 3'-terminal segments since preparations lose the capacity to modify the two termini with an identical first order thermal decay rate. Certain features of the rRNA precursor which may be involved in cognitive interaction with RNase M5 are discussed.

Ammonia↗